With Superman off-world, Supergirl becomes a worldwide beacon of hope. Meanwhile, Lena takes secret measures to keep James out of prison, while Kara welcomes a new report to CatCo and Alex and Brainiac-5 get off to a rocky start after the latter takes Winn's position at the DEO.

The U.S. people are shaken by the revelation that the President is an alien. As Supergirl tries to quell the unrest, Nia tells James that he should write an editorial supporting aliens. Meanwhile, Mercy launches an attack on L-Corp to shut down the image inducers and reveal the aliens for who they really are.

To heal Supergirl, Alex assigns Brainiac-5 and Lena to find a way to remove the Kryptonite from Earth's atmosphere. Meanwhile, Mercy and Otis abduct aliens from a DEO facility and use them to attack children and spread fear, and Hank meets an ally in his fight.

When Jensen--the new Parasite--attacks aliens, Supergirl is forced to take to the sidelines rather than give him further power. As a result, Kara writes an article on an alien healer who makes him a target. Meanwhile, Alex learns some surprising things about her new superior, and James comes to a realization about the Children of Liberty and their anti-alien agenda.

As the Thanksgiving holiday approaches, the Children of Liberty prepare a new initiative to wipe out the aliens among them. James and Lena have their first major argument, and Nia displays narcolepsy but refuses help.

Hank assures Supergirl that Manchester is a trustworthy ally. Meanwhile, James meets with Agent Liberty and has to choose between betraying his reputation or committing an act of terrorism for the Children of Liberty.

Deegan "thinks big" and rewrites the reality of Earth-1 so that he's the only superhero... and a familiar face. While Barry and Oliver try to contact Superman on Earth-38, Kara tries to get through to her foster sister Alex... who no longer remembers who Kara is.

Supergirl finds a ship full of dead SEAL soldiers, and discovers that it's connected to Haley and the US government. Brainiac-5 sets up a meeting—at a romantic restaurant—with Nia to discuss her future as a possible superhero, and Lena tells James what she's been working on.

Kara travels with Nia to the latter's hometown and discovers that Nia is inheriting the Dreamer power from her mother... which has skipped Nia's sister Maeve. In National City, an outbreak of a new drug rage starts and Alex investigates while asking J'onn to determine if she's having memory problems.

Kara continues to deal with the fallout from Alex's mindwipe, and a new villain enters National City: Menagerie, a human jewel thief merged with an alien symbiote. Nia invites Brainiac-5 to her Valentine's Day party, and Ben reaches out to his wife and son.

Ben proposes to end the Alien Amnesty Act and holds a rally. Alien protesters hold a peaceful march, but Manchester plans to disrupt the event using stolen Kryptonian technology... and reveal J'onn's true feelings. James goes to the rally to cover events as a photographer.

James undergoes surgery to replace his shattered spine, and Lena has no choice but to work with her brother Lex to perfect the Harun-El serum to cure James before he dies. J'onn and Kara track down Manchester, who has recovered the Staff of H'ronmeer and attempts to turn J'onn from the path of peace.

Lex spends three years plotting his next scheme, working with the Kaznian government to train the Supergirl clone to further their ambitions against America so that he can step in and stop them, becoming a hero to the world and its savior.

Supergirl and Lena go to Stryker's Island to check out Lex's cell, and find a clue to his schemes. Supergirl is declared a criminal and is forced to question whether she does more harm or good, while James deals with the fallout from being injected with the serum.

Kara and Lena head to Kaznia to hunt down Lex. However, Eve Tessmacher sets a trap for the duo that could ultimately reveal that Kara is Supergirl. Meanwhile, Alex gets a long-awaited phone call, James practices using his powers, and Ben Lockwood takes a dangerous stand inside the DEO.

Kara comes face to face with Red Daughter and the two engage in an epic battle. Determined to find a way to extract the Harun-El, Lena turns to an unlikely source for help - Lillian Luthor. Meanwhile, Alex realizes she's missing parts of her memory, and Brainy, Nia and J'onn set out to track down aliens who have been abducted by.